README.Rmd

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# chirpR: tools for automated acoustic analyses in R

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## Description

`chirpR` is a work in progress. Originally being built for internal use only, I decided that maybe there are others that would benifit from this tool.

`chirpR` is an R package that simplifies the process of analyzing and interpreting bird acoustic monitoring data. It provides a user-friendly wrapper for [BirdNet-Analyzer](https://github.com/kahst/BirdNET-Analyzer) and [ecoVAD](https://github.com/NINAnor/ecoVAD), allowing users to easily install and run BirdNet and ecoVAD directly from R. Additionally, `chirpR` includes a collection of functions for analyzing and visualizing BirdNet output. Developed with a semi-automated analysis pipeline in mind, `chirpR` streamlines the analysis process.

## About

Developed by 🦜Andrew Fairbairn

Current lab: [Chair for Terrestrial Ecology](https://www3.ls.tum.de/en/toek/home/), Technical University of Munich

[Homepage](https://afairbairn.com/)


## Installation

You can install chirpR from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("AFairbairn/chirpR")
```

`chirpR` requires Python 3.8 <= 3.10
To install a supported version of Python, head over to https://www.python.org/, hover over downloads, select your operating system and then scroll down to the installer for a supported version of python. Download and follow the installation instructions. Be sure at add Python to your systems PATH. This is usually an option during installation, but if not do a search for adding Python to PATH of your particular operating system.

## BirdNet Example

Installing and running BirdNet:

```{r, cache = TRUE}
library(chirpR)

## Install BirdNet
birdNet.install()

## Run BirdNet using default settings
## i is the input files path, as in BirdNet-Analyze
results <- birdNet.analyze(i="E:/acoustic recordings", o="E:/bnResults")
head(results[,c(4:6)])
```

:warning: **If you are using Linux or RStudio Server**  There is an issue where  birdNet.analyze() may not find the location of the birdNET installation. If birdNet.install() runs correctly and you run into this issue, please add path="{path.to.R.packages}/chirpR/birdNet/BirdNET-Analyzer-main" to birdNet.analyze().

## ecoVAD Example

Setup ecoVAD:

```{r, cache = TRUE}
library(chirpR)

## Setup ecoVad
#ecoVAD.setup()

```

### Training ecoVAD models

The developers of [ecoVAD](https://github.com/NINAnor/ecoVAD) recommend training using the OpenSLR LibriSpeech English language library. As a service for our users, I thought that I would provide a list to several speech libraries for different languages below. This is not an exhaustive list and I would appreciate submission of additional resources. Just contact me!

* English
    + [LibriSpeech ASR corpus](https://www.openslr.org/12/)
* German
    + [LibriVoxDeEn](https://www.cl.uni-heidelberg.de/statnlpgroup/librivoxdeen/)
    + [LibriVox MP3 bundle](https://www.ce.cit.tum.de/mmk/verschiedenes/german-speech-corpus-aligned-with-ctc-segmentation/)
* Multilingual
    + [Mozilla common voice](https://commonvoice.mozilla.org/en/datasets)